A mass spectrometry imaging toolbox for statistical analysis

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Documentation for package ‘Cardinal’ version 2.0.2

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Cardinal-package Mass spectrometry imaging tools

-- A --

abstract-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
alpha.colors Color palettes for imaging
annotatedDataFrameFrom-method ImageData: Class containing arrays of imaging data
as.env-method MassDataFrame: data frame with mass-to-charge ratio metadata
as.env-method PositionDataFrame: data frame with spatial position metadata
as.env-method XDataFrame: DataFrame with eXtra metadata columns
as.list-method ImageList: Abstract image data list
as.list-method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
as.list-method MassDataFrame: data frame with mass-to-charge ratio metadata
as.list-method PositionDataFrame: data frame with spatial position metadata

-- B --

baselineReduction MSImageProcess: Class containing mass spectral preprocessing information
baselineReduction-method MSImageProcess: Class containing mass spectral preprocessing information
baselineReduction-method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
baselineReduction<- MSImageProcess: Class containing mass spectral preprocessing information
baselineReduction<--method MSImageProcess: Class containing mass spectral preprocessing information
baselineReduction<--method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
batchProcess Batch Pre-Processing on an Imaging Dataset
batchProcess-method Batch Pre-Processing on an Imaging Dataset
batchProcess-methods Batch Pre-Processing on an Imaging Dataset
Binmat Binmat: On-disk matrix class using on-demand disk access
Binmat-class Binmat: On-disk matrix class using on-demand disk access
bw.colors Color palettes for imaging

-- C --

Cardinal Mass spectrometry imaging tools
Cardinal-deprecated Deprecated functions and methods in Cardinal
Cardinal-reexports Objects exported from other packages
cbind-method Binmat: On-disk matrix class using on-demand disk access
cbind-method Hashmat: Sparse matrix class using lists as hash tables
cbind-method ImageList: Abstract image data list
cbind-method MSImagingExperiment: Mass spectrometry imaging experiments
cbind-method MassDataFrame: data frame with mass-to-charge ratio metadata
cbind-method PositionDataFrame: data frame with spatial position metadata
cbind-method SparseImagingExperiment: Pixel-sparse imaging experiments
cbind-method XDataFrame: DataFrame with eXtra metadata columns
centroided MSImageProcess: Class containing mass spectral preprocessing information
centroided-method MSImageProcess: Class containing mass spectral preprocessing information
centroided-method MSImageSet: Class to contain mass spectrometry imaging experiment data
centroided-method MSImagingExperiment: Mass spectrometry imaging experiments
centroided<- MSImageProcess: Class containing mass spectral preprocessing information
centroided<--method MSImageProcess: Class containing mass spectral preprocessing information
centroided<--method MSImageSet: Class to contain mass spectrometry imaging experiment data
centroided<--method MSImagingExperiment: Mass spectrometry imaging experiments
class:Binmat Binmat: On-disk matrix class using on-demand disk access
class:Hashmat Hashmat: Sparse matrix class using lists as hash tables
class:IAnnotatedDataFrame IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
class:ImageArrayList ImageList: Abstract image data list
class:ImageData ImageData: Class containing arrays of imaging data
class:ImageList ImageList: Abstract image data list
class:ImagingExperiment ImagingExperiment: Abstract class for imaging experiments
class:iSet iSet: Class to contain high-throughput imaging experiment data and metadata
class:MassDataFrame MassDataFrame: data frame with mass-to-charge ratio metadata
class:MIAPE-Imaging MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
class:MSContinuousImagingExperiment MSContinuousImagingExperiment: Dense mass spectrometry imaging experiments
class:MSContinuousImagingSpectraList ImageList: Abstract image data list
class:MSImageData MSImageData: Class containing mass spectrometry image data
class:MSImageProcess MSImageProcess: Class containing mass spectral preprocessing information
class:MSImageSet MSImageSet: Class to contain mass spectrometry imaging experiment data
class:MSImagingExperiment MSImagingExperiment: Mass spectrometry imaging experiments
class:MSImagingInfo MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
class:MSProcessedImagingExperiment MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
class:MSProcessedImagingSpectraList ImageList: Abstract image data list
class:OPLS Orthogonal partial least squares
class:PCA Principal components analysis
class:PLS Partial least squares
class:PositionDataFrame PositionDataFrame: data frame with spatial position metadata
class:ResultSet ResultSet: Class to contain analysis results for imaging experiments
class:SImageData SImageData: Class containing sparse image data
class:SImageSet SIMageSet: Class to contain pixel-sparse imaging data
class:SimpleImageArrayList ImageList: Abstract image data list
class:SimpleImageList ImageList: Abstract image data list
class:SparseImagingExperiment SparseImagingExperiment: Pixel-sparse imaging experiments
class:SpatialKMeans Spatially-aware k-means clustering
class:SpatialShrunkenCentroids Spatially-aware shrunken centroid clustering and classification
class:XDataFrame XDataFrame: DataFrame with eXtra metadata columns
colnames-method Binmat: On-disk matrix class using on-demand disk access
colnames-method Hashmat: Sparse matrix class using lists as hash tables
colnames<--method Binmat: On-disk matrix class using on-demand disk access
colnames<--method Hashmat: Sparse matrix class using lists as hash tables
color.map Color palettes for imaging
combine-method Hashmat: Sparse matrix class using lists as hash tables
combine-method IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
combine-method ImageData: Class containing arrays of imaging data
combine-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
combine-method MSImageProcess: Class containing mass spectral preprocessing information
combine-method MSImageSet: Class to contain mass spectrometry imaging experiment data
combine-method SImageData: Class containing sparse image data
combine-method SIMageSet: Class to contain pixel-sparse imaging data
combine-method iSet: Class to contain high-throughput imaging experiment data and metadata
combiner-method MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
combiner<--method MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
coord PositionDataFrame: data frame with spatial position metadata
coord-method IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
coord-method PositionDataFrame: data frame with spatial position metadata
coord-method SImageData: Class containing sparse image data
coord-method SparseImagingExperiment: Pixel-sparse imaging experiments
coord-method iSet: Class to contain high-throughput imaging experiment data and metadata
coord-methods PositionDataFrame: data frame with spatial position metadata
coord<- PositionDataFrame: data frame with spatial position metadata
coord<--method IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
coord<--method PositionDataFrame: data frame with spatial position metadata
coord<--method SImageData: Class containing sparse image data
coord<--method SIMageSet: Class to contain pixel-sparse imaging data
coord<--method SparseImagingExperiment: Pixel-sparse imaging experiments
coord<--method iSet: Class to contain high-throughput imaging experiment data and metadata
coordinates PositionDataFrame: data frame with spatial position metadata
coordinates-method PositionDataFrame: data frame with spatial position metadata
coordinates-method SparseImagingExperiment: Pixel-sparse imaging experiments
coordinates-methods PositionDataFrame: data frame with spatial position metadata
coordinates<- PositionDataFrame: data frame with spatial position metadata
coordinates<--method PositionDataFrame: data frame with spatial position metadata
coordinates<--method SparseImagingExperiment: Pixel-sparse imaging experiments
coordLabels PositionDataFrame: data frame with spatial position metadata
coordLabels-method IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
coordLabels-method PositionDataFrame: data frame with spatial position metadata
coordLabels-method SparseImagingExperiment: Pixel-sparse imaging experiments
coordLabels-method iSet: Class to contain high-throughput imaging experiment data and metadata
coordLabels-methods PositionDataFrame: data frame with spatial position metadata
coordLabels<- PositionDataFrame: data frame with spatial position metadata
coordLabels<--method IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
coordLabels<--method PositionDataFrame: data frame with spatial position metadata
coordLabels<--method SIMageSet: Class to contain pixel-sparse imaging data
coordLabels<--method SparseImagingExperiment: Pixel-sparse imaging experiments
coordLabels<--method iSet: Class to contain high-throughput imaging experiment data and metadata
coordnames PositionDataFrame: data frame with spatial position metadata
coordnames-method PositionDataFrame: data frame with spatial position metadata
coordnames-method SparseImagingExperiment: Pixel-sparse imaging experiments
coordnames-methods PositionDataFrame: data frame with spatial position metadata
coordnames<- PositionDataFrame: data frame with spatial position metadata
coordnames<--method PositionDataFrame: data frame with spatial position metadata
coordnames<--method SparseImagingExperiment: Pixel-sparse imaging experiments
coregister Coregister images
coregister-method Coregister images
coregister-methods Coregister images
cvApply Apply cross-validation to imaging analyses
cvApply-method Apply cross-validation to imaging analyses
cvApply-methods Apply cross-validation to imaging analyses

-- D --

dim-method Binmat: On-disk matrix class using on-demand disk access
dim-method Hashmat: Sparse matrix class using lists as hash tables
dim-method ImageData: Class containing arrays of imaging data
dim-method ImageList: Abstract image data list
dim-method ImagingExperiment: Abstract class for imaging experiments
dim-method SImageData: Class containing sparse image data
dim-method iSet: Class to contain high-throughput imaging experiment data and metadata
dim<--method Binmat: On-disk matrix class using on-demand disk access
dim<--method Hashmat: Sparse matrix class using lists as hash tables
dimnames-method Binmat: On-disk matrix class using on-demand disk access
dimnames-method Hashmat: Sparse matrix class using lists as hash tables
dimnames-method ImagingExperiment: Abstract class for imaging experiments
dimnames<--method Binmat: On-disk matrix class using on-demand disk access
dimnames<--method Hashmat: Sparse matrix class using lists as hash tables
dims-method ImageData: Class containing arrays of imaging data
dims-method ImageList: Abstract image data list
dims-method PositionDataFrame: data frame with spatial position metadata
dims-method SImageData: Class containing sparse image data
dims-method SparseImagingExperiment: Pixel-sparse imaging experiments
dims-method iSet: Class to contain high-throughput imaging experiment data and metadata
discrete.colors Color palettes for imaging
divergent.colors Color palettes for imaging

-- E --

embeddingMethod MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
embeddingMethod-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
embeddingMethod<- MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
embeddingMethod<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
experimentData-method iSet: Class to contain high-throughput imaging experiment data and metadata
experimentData<--method iSet: Class to contain high-throughput imaging experiment data and metadata
expinfo-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information

-- F --

fData ImagingExperiment: Abstract class for imaging experiments
fData-method ImagingExperiment: Abstract class for imaging experiments
fData-method iSet: Class to contain high-throughput imaging experiment data and metadata
fData-methods ImagingExperiment: Abstract class for imaging experiments
fData<- ImagingExperiment: Abstract class for imaging experiments
fData<--method ImagingExperiment: Abstract class for imaging experiments
fData<--method iSet: Class to contain high-throughput imaging experiment data and metadata
featureApply Apply functions over imaging datasets
featureApply-method Apply functions over imaging datasets
featureApply-methods Apply functions over imaging datasets
featureData ImagingExperiment: Abstract class for imaging experiments
featureData-method ImagingExperiment: Abstract class for imaging experiments
featureData-method iSet: Class to contain high-throughput imaging experiment data and metadata
featureData-methods ImagingExperiment: Abstract class for imaging experiments
featureData<- ImagingExperiment: Abstract class for imaging experiments
featureData<--method ImagingExperiment: Abstract class for imaging experiments
featureData<--method iSet: Class to contain high-throughput imaging experiment data and metadata
featureNames ImagingExperiment: Abstract class for imaging experiments
featureNames-method ImagingExperiment: Abstract class for imaging experiments
featureNames-method SImageData: Class containing sparse image data
featureNames-method iSet: Class to contain high-throughput imaging experiment data and metadata
featureNames-methods ImagingExperiment: Abstract class for imaging experiments
featureNames<- ImagingExperiment: Abstract class for imaging experiments
featureNames<--method ImagingExperiment: Abstract class for imaging experiments
featureNames<--method SImageData: Class containing sparse image data
featureNames<--method SIMageSet: Class to contain pixel-sparse imaging data
featureNames<--method iSet: Class to contain high-throughput imaging experiment data and metadata
features ImagingExperiment: Abstract class for imaging experiments
features-method ImagingExperiment: Abstract class for imaging experiments
features-method MSImageSet: Class to contain mass spectrometry imaging experiment data
features-method MSImagingExperiment: Mass spectrometry imaging experiments
features-method iSet: Class to contain high-throughput imaging experiment data and metadata
features-methods ImagingExperiment: Abstract class for imaging experiments
files MSImageProcess: Class containing mass spectral preprocessing information
files-method MSImageProcess: Class containing mass spectral preprocessing information
files<- MSImageProcess: Class containing mass spectral preprocessing information
files<--method MSImageProcess: Class containing mass spectral preprocessing information
filter-method Data transformation and summarization for imaging experiments
fvarLabels-method iSet: Class to contain high-throughput imaging experiment data and metadata
fvarLabels<--method iSet: Class to contain high-throughput imaging experiment data and metadata
fvarMetadata-method iSet: Class to contain high-throughput imaging experiment data and metadata
fvarMetadata<--method iSet: Class to contain high-throughput imaging experiment data and metadata

-- G --

generateImage Generate a simulated image
generateSpectrum Generate a simulated spectrum
gradient.colors Color palettes for imaging
gridded-method PositionDataFrame: data frame with spatial position metadata
gridded-method SparseImagingExperiment: Pixel-sparse imaging experiments
gridded<--method PositionDataFrame: data frame with spatial position metadata
gridded<--method SparseImagingExperiment: Pixel-sparse imaging experiments

-- H --

Hashmat Hashmat: Sparse matrix class using lists as hash tables
Hashmat-class Hashmat: Sparse matrix class using lists as hash tables

-- I --

IAnnotatedDataFrame IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
IAnnotatedDataFrame-class IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
iData ImagingExperiment: Abstract class for imaging experiments
iData-method ImagingExperiment: Abstract class for imaging experiments
iData-method SImageData: Class containing sparse image data
iData-method SIMageSet: Class to contain pixel-sparse imaging data
iData-method iSet: Class to contain high-throughput imaging experiment data and metadata
iData-methods ImagingExperiment: Abstract class for imaging experiments
iData<- ImagingExperiment: Abstract class for imaging experiments
iData<--method ImagingExperiment: Abstract class for imaging experiments
iData<--method MSContinuousImagingExperiment: Dense mass spectrometry imaging experiments
iData<--method MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
iData<--method SImageData: Class containing sparse image data
iData<--method SIMageSet: Class to contain pixel-sparse imaging data
iData<--method iSet: Class to contain high-throughput imaging experiment data and metadata
image Plot the pixel data of an imaging dataset
image-method Plot the pixel data of an imaging dataset
image-methods Plot the pixel data of an imaging dataset
image3D Plot the pixel data of an imaging dataset
image3D-method Plot the pixel data of an imaging dataset
image3D-methods Plot the pixel data of an imaging dataset
ImageArrayList ImageList: Abstract image data list
ImageArrayList-class ImageList: Abstract image data list
ImageData ImageData: Class containing arrays of imaging data
imageData ImagingExperiment: Abstract class for imaging experiments
ImageData-class ImageData: Class containing arrays of imaging data
imageData-method ImagingExperiment: Abstract class for imaging experiments
imageData-method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
imageData-method iSet: Class to contain high-throughput imaging experiment data and metadata
imageData-methods ImagingExperiment: Abstract class for imaging experiments
imageData<- ImagingExperiment: Abstract class for imaging experiments
imageData<--method ImagingExperiment: Abstract class for imaging experiments
imageData<--method MSContinuousImagingExperiment: Dense mass spectrometry imaging experiments
imageData<--method MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
imageData<--method iSet: Class to contain high-throughput imaging experiment data and metadata
ImageList ImageList: Abstract image data list
ImageList-class ImageList: Abstract image data list
imageShape MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
imageShape-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
imageShape<- MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
imageShape<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
ImagingExperiment ImagingExperiment: Abstract class for imaging experiments
ImagingExperiment-class ImagingExperiment: Abstract class for imaging experiments
initialize-method Binmat: On-disk matrix class using on-demand disk access
initialize-method Hashmat: Sparse matrix class using lists as hash tables
initialize-method IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
initialize-method ImageData: Class containing arrays of imaging data
initialize-method MSImageData: Class containing mass spectrometry image data
initialize-method MSImageProcess: Class containing mass spectral preprocessing information
initialize-method MSImageSet: Class to contain mass spectrometry imaging experiment data
initialize-method MassDataFrame: data frame with mass-to-charge ratio metadata
initialize-method PositionDataFrame: data frame with spatial position metadata
initialize-method SImageData: Class containing sparse image data
initialize-method SIMageSet: Class to contain pixel-sparse imaging data
initialize-method iSet: Class to contain high-throughput imaging experiment data and metadata
inSituChemistry MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
inSituChemistry-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
inSituChemistry<- MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
inSituChemistry<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
instrumentModel MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
instrumentModel-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
instrumentModel-method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
instrumentModel<- MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
instrumentModel<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
instrumentModel<--method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
instrumentVendor MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
instrumentVendor-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
instrumentVendor-method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
instrumentVendor<- MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
instrumentVendor<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
instrumentVendor<--method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
intensity.colors Color palettes for imaging
ionizationType MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
ionizationType-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
ionizationType-method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
ionizationType<- MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
ionizationType<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
ionizationType<--method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
iSet iSet: Class to contain high-throughput imaging experiment data and metadata
iSet-class iSet: Class to contain high-throughput imaging experiment data and metadata

-- J --

jet.colors Color palettes for imaging

-- K --

keys Hashmat: Sparse matrix class using lists as hash tables
keys-method Hashmat: Sparse matrix class using lists as hash tables
keys-method MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
keys<- Hashmat: Sparse matrix class using lists as hash tables
keys<--method Hashmat: Sparse matrix class using lists as hash tables
keys<--method MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments

-- L --

lapply-method XDataFrame: DataFrame with eXtra metadata columns
length-method ImageList: Abstract image data list
length-method ImagingExperiment: Abstract class for imaging experiments
length-method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
length-method ResultSet: Class to contain analysis results for imaging experiments
length-method XDataFrame: DataFrame with eXtra metadata columns
lineScanDirection MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
lineScanDirection-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
lineScanDirection-method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
lineScanDirection<- MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
lineScanDirection<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
lineScanDirection<--method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
logLik-method Spatially-aware shrunken centroid clustering and classification

-- M --

massAnalyzerType MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
massAnalyzerType-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
massAnalyzerType-method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
massAnalyzerType<- MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
massAnalyzerType<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
massAnalyzerType<--method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
MassDataFrame MassDataFrame: data frame with mass-to-charge ratio metadata
MassDataFrame-class MassDataFrame: data frame with mass-to-charge ratio metadata
matrixApplication MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
matrixApplication-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
matrixApplication-method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
matrixApplication<- MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
matrixApplication<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
matrixApplication<--method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
MIAPE-Imaging MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
MIAPE-Imaging-class MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
modelData ResultSet: Class to contain analysis results for imaging experiments
modelData-method ResultSet: Class to contain analysis results for imaging experiments
modelData<- ResultSet: Class to contain analysis results for imaging experiments
modelData<--method ResultSet: Class to contain analysis results for imaging experiments
MSContinuousImagingExperiment MSContinuousImagingExperiment: Dense mass spectrometry imaging experiments
MSContinuousImagingExperiment-class MSContinuousImagingExperiment: Dense mass spectrometry imaging experiments
MSContinuousImagingSpectraList ImageList: Abstract image data list
MSContinuousImagingSpectraList-class ImageList: Abstract image data list
msiInfo MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
msiInfo-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
msiInfo-method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
MSImageData MSImageData: Class containing mass spectrometry image data
MSImageData-class MSImageData: Class containing mass spectrometry image data
MSImageProcess MSImageProcess: Class containing mass spectral preprocessing information
MSImageProcess-class MSImageProcess: Class containing mass spectral preprocessing information
MSImageSet MSImageSet: Class to contain mass spectrometry imaging experiment data
MSImageSet-class MSImageSet: Class to contain mass spectrometry imaging experiment data
MSImagingExperiment MSImagingExperiment: Mass spectrometry imaging experiments
MSImagingExperiment-class MSImagingExperiment: Mass spectrometry imaging experiments
MSImagingInfo MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
MSImagingInfo-class MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
MSProcessedImagingExperiment MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
MSProcessedImagingExperiment-class MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
MSProcessedImagingSpectraList ImageList: Abstract image data list
MSProcessedImagingSpectraList-class ImageList: Abstract image data list
mutate-method Data transformation and summarization for imaging experiments
mz Manipulate mass-to-charge-ratio values
mz-method MSImageSet: Class to contain mass spectrometry imaging experiment data
mz-method MSImagingExperiment: Mass spectrometry imaging experiments
mz-method MassDataFrame: data frame with mass-to-charge ratio metadata
mz-method Manipulate mass-to-charge-ratio values
mz-methods Manipulate mass-to-charge-ratio values
mz<- Manipulate mass-to-charge-ratio values
mz<--method MSImageSet: Class to contain mass spectrometry imaging experiment data
mz<--method MSImagingExperiment: Mass spectrometry imaging experiments
mz<--method MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
mz<--method MassDataFrame: data frame with mass-to-charge ratio metadata
mzData MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
mzData-method MSImageData: Class containing mass spectrometry image data
mzData-method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
mzData-method MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
mzData-method SImageData: Class containing sparse image data
mzData-methods MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
mzData<- MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
mzData<--method MSImageData: Class containing mass spectrometry image data
mzData<--method MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
mzData<--method SImageData: Class containing sparse image data

-- N --

names-method ImageData: Class containing arrays of imaging data
names-method ImageList: Abstract image data list
names-method ResultSet: Class to contain analysis results for imaging experiments
names-method XDataFrame: DataFrame with eXtra metadata columns
names<--method ImageData: Class containing arrays of imaging data
names<--method ImageList: Abstract image data list
normalization MSImageProcess: Class containing mass spectral preprocessing information
normalization-method MSImageProcess: Class containing mass spectral preprocessing information
normalization-method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
normalization<- MSImageProcess: Class containing mass spectral preprocessing information
normalization<--method MSImageProcess: Class containing mass spectral preprocessing information
normalization<--method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
normalize Normalize an imaging dataset
normalize-method Normalize an imaging dataset
normalize-methods Normalize an imaging dataset
normalize.tic Normalize an imaging dataset
notes-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
notes<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information

-- O --

OPLS Orthogonal partial least squares
OPLS-class Orthogonal partial least squares
OPLS-method Orthogonal partial least squares
OPLS-methods Orthogonal partial least squares
otherInfo-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information

-- P --

PCA Principal components analysis
PCA-class Principal components analysis
PCA-method Principal components analysis
PCA-methods Principal components analysis
pData ImagingExperiment: Abstract class for imaging experiments
pData-method Hashmat: Sparse matrix class using lists as hash tables
pData-method ImagingExperiment: Abstract class for imaging experiments
pData-method iSet: Class to contain high-throughput imaging experiment data and metadata
pData-methods ImagingExperiment: Abstract class for imaging experiments
pData<- ImagingExperiment: Abstract class for imaging experiments
pData<--method Hashmat: Sparse matrix class using lists as hash tables
pData<--method ImagingExperiment: Abstract class for imaging experiments
pData<--method iSet: Class to contain high-throughput imaging experiment data and metadata
peakAlign Peak align an imaging dataset
peakAlign-method Peak align an imaging dataset
peakAlign-methods Peak align an imaging dataset
peakAlign.diff Peak align an imaging dataset
peakAlign.DP Peak align an imaging dataset
peakBin Peak bin an imaging dataset
peakBin-method Peak bin an imaging dataset
peakBin-methods Peak bin an imaging dataset
peakData MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
peakData-method MSImageData: Class containing mass spectrometry image data
peakData-method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
peakData-method MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
peakData-method SImageData: Class containing sparse image data
peakData-methods MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
peakData<- MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
peakData<--method MSImageData: Class containing mass spectrometry image data
peakData<--method MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
peakData<--method SImageData: Class containing sparse image data
peakFilter Peak filter an imaging dataset
peakFilter-method Peak filter an imaging dataset
peakFilter-methods Peak filter an imaging dataset
peakFilter.freq Peak filter an imaging dataset
peakPick Peak pick an imaging dataset
peakPick-method Peak pick an imaging dataset
peakPick-methods Peak pick an imaging dataset
peakPick.adaptive Peak pick an imaging dataset
peakPick.limpic Peak pick an imaging dataset
peakPick.simple Peak pick an imaging dataset
peakPicking MSImageProcess: Class containing mass spectral preprocessing information
peakPicking-method MSImageProcess: Class containing mass spectral preprocessing information
peakPicking-method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
peakPicking<- MSImageProcess: Class containing mass spectral preprocessing information
peakPicking<--method MSImageProcess: Class containing mass spectral preprocessing information
peakPicking<--method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
peaks MSImagingExperiment: Mass spectrometry imaging experiments
peaks-method MSImageSet: Class to contain mass spectrometry imaging experiment data
peaks-method MSImagingExperiment: Mass spectrometry imaging experiments
peaks-methods MSImagingExperiment: Mass spectrometry imaging experiments
peaks<- MSImagingExperiment: Mass spectrometry imaging experiments
peaks<--method MSImageSet: Class to contain mass spectrometry imaging experiment data
peaks<--method MSImagingExperiment: Mass spectrometry imaging experiments
pixelApply Apply functions over imaging datasets
pixelApply-method Apply functions over imaging datasets
pixelApply-methods Apply functions over imaging datasets
pixelData ImagingExperiment: Abstract class for imaging experiments
pixelData-method ImagingExperiment: Abstract class for imaging experiments
pixelData-method iSet: Class to contain high-throughput imaging experiment data and metadata
pixelData-methods ImagingExperiment: Abstract class for imaging experiments
pixelData<- ImagingExperiment: Abstract class for imaging experiments
pixelData<--method ImagingExperiment: Abstract class for imaging experiments
pixelData<--method iSet: Class to contain high-throughput imaging experiment data and metadata
pixelNames ImagingExperiment: Abstract class for imaging experiments
pixelNames-method IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
pixelNames-method ImagingExperiment: Abstract class for imaging experiments
pixelNames-method SImageData: Class containing sparse image data
pixelNames-method iSet: Class to contain high-throughput imaging experiment data and metadata
pixelNames-methods ImagingExperiment: Abstract class for imaging experiments
pixelNames<- ImagingExperiment: Abstract class for imaging experiments
pixelNames<--method IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
pixelNames<--method ImagingExperiment: Abstract class for imaging experiments
pixelNames<--method SImageData: Class containing sparse image data
pixelNames<--method SIMageSet: Class to contain pixel-sparse imaging data
pixelNames<--method iSet: Class to contain high-throughput imaging experiment data and metadata
pixels ImagingExperiment: Abstract class for imaging experiments
pixels-method ImagingExperiment: Abstract class for imaging experiments
pixels-method MSImageSet: Class to contain mass spectrometry imaging experiment data
pixels-method MSImagingExperiment: Mass spectrometry imaging experiments
pixels-method iSet: Class to contain high-throughput imaging experiment data and metadata
pixels-methods ImagingExperiment: Abstract class for imaging experiments
pixelSize MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
pixelSize-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
pixelSize-method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
pixelSize<- MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
pixelSize<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
pixelSize<--method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
plot Plot the feature data of an imaging dataset
plot-method Plot the feature data of an imaging dataset
plot-methods Plot the feature data of an imaging dataset
plot.summary.CrossValidated Apply cross-validation to imaging analyses
plot.summary.OPLS Orthogonal partial least squares
plot.summary.PCA Principal components analysis
plot.summary.PLS Partial least squares
plot.summary.SpatialKMeans Spatially-aware k-means clustering
plot.summary.SpatialShrunkenCentroids Spatially-aware shrunken centroid clustering and classification
PLS Partial least squares
PLS-class Partial least squares
PLS-method Partial least squares
PLS-methods Partial least squares
positionArray SImageData: Class containing sparse image data
positionArray-method SImageData: Class containing sparse image data
positionArray<- SImageData: Class containing sparse image data
positionArray<--method SImageData: Class containing sparse image data
PositionDataFrame PositionDataFrame: data frame with spatial position metadata
PositionDataFrame-class PositionDataFrame: data frame with spatial position metadata
predict-method Orthogonal partial least squares
predict-method Principal components analysis
predict-method Partial least squares
predict-method Spatially-aware shrunken centroid clustering and classification
preproc-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
preproc-method SparseImagingExperiment: Pixel-sparse imaging experiments
preproc<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
print.summary.CrossValidated Apply cross-validation to imaging analyses
print.summary.iSet iSet: Class to contain high-throughput imaging experiment data and metadata
print.summary.OPLS Orthogonal partial least squares
print.summary.PCA Principal components analysis
print.summary.PLS Partial least squares
print.summary.SpatialKMeans Spatially-aware k-means clustering
print.summary.SpatialShrunkenCentroids Spatially-aware shrunken centroid clustering and classification
process Delayed Processing of Imaging Datasets
process-method Delayed Processing of Imaging Datasets
process-methods Delayed Processing of Imaging Datasets
processingData MSImageSet: Class to contain mass spectrometry imaging experiment data
processingData-method MSImageSet: Class to contain mass spectrometry imaging experiment data
processingData-method SparseImagingExperiment: Pixel-sparse imaging experiments
processingData-methods MSImageSet: Class to contain mass spectrometry imaging experiment data
processingData<- MSImageSet: Class to contain mass spectrometry imaging experiment data
processingData<--method MSImageSet: Class to contain mass spectrometry imaging experiment data
processingData<--method SparseImagingExperiment: Pixel-sparse imaging experiments
prochistory MSImageProcess: Class containing mass spectral preprocessing information
prochistory-method MSImageProcess: Class containing mass spectral preprocessing information
prochistory<- MSImageProcess: Class containing mass spectral preprocessing information
prochistory<--method MSImageProcess: Class containing mass spectral preprocessing information
protocolData-method iSet: Class to contain high-throughput imaging experiment data and metadata
protocolData<--method iSet: Class to contain high-throughput imaging experiment data and metadata
pubMedIds-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
pubMedIds<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information

-- R --

rbind-method Binmat: On-disk matrix class using on-demand disk access
rbind-method Hashmat: Sparse matrix class using lists as hash tables
rbind-method ImageList: Abstract image data list
rbind-method MSImagingExperiment: Mass spectrometry imaging experiments
rbind-method MassDataFrame: data frame with mass-to-charge ratio metadata
rbind-method PositionDataFrame: data frame with spatial position metadata
rbind-method SparseImagingExperiment: Pixel-sparse imaging experiments
rbind-method XDataFrame: DataFrame with eXtra metadata columns
readAnalyze Read mass spectrometry imaging data files
readImzML Read mass spectrometry imaging data files
readMSIData Read mass spectrometry imaging data files
reduceBaseline Reduce the baseline for an imaging dataset
reduceBaseline-method Reduce the baseline for an imaging dataset
reduceBaseline-methods Reduce the baseline for an imaging dataset
reduceBaseline.median Reduce the baseline for an imaging dataset
reduceDimension Reduce the dimension of an imaging dataset
reduceDimension-method Reduce the dimension of an imaging dataset
reduceDimension-methods Reduce the dimension of an imaging dataset
reduceDimension.bin Reduce the dimension of an imaging dataset
reduceDimension.peaks Reduce the dimension of an imaging dataset
reduceDimension.resample Reduce the dimension of an imaging dataset
regeneratePositions SImageData: Class containing sparse image data
regeneratePositions-method SImageData: Class containing sparse image data
regeneratePositions-method SIMageSet: Class to contain pixel-sparse imaging data
resolution PositionDataFrame: data frame with spatial position metadata
resolution-method MassDataFrame: data frame with mass-to-charge ratio metadata
resolution-method PositionDataFrame: data frame with spatial position metadata
resolution-method SparseImagingExperiment: Pixel-sparse imaging experiments
resolution<- PositionDataFrame: data frame with spatial position metadata
resolution<--method MassDataFrame: data frame with mass-to-charge ratio metadata
resolution<--method PositionDataFrame: data frame with spatial position metadata
resolution<--method SparseImagingExperiment: Pixel-sparse imaging experiments
resultData ResultSet: Class to contain analysis results for imaging experiments
resultData-method ResultSet: Class to contain analysis results for imaging experiments
resultData<- ResultSet: Class to contain analysis results for imaging experiments
resultData<--method ResultSet: Class to contain analysis results for imaging experiments
ResultSet ResultSet: Class to contain analysis results for imaging experiments
ResultSet-class ResultSet: Class to contain analysis results for imaging experiments
risk.colors Color palettes for imaging
rownames-method Binmat: On-disk matrix class using on-demand disk access
rownames-method Hashmat: Sparse matrix class using lists as hash tables
rownames<--method Binmat: On-disk matrix class using on-demand disk access
rownames<--method Hashmat: Sparse matrix class using lists as hash tables
run PositionDataFrame: data frame with spatial position metadata
run-method PositionDataFrame: data frame with spatial position metadata
run-method SparseImagingExperiment: Pixel-sparse imaging experiments
run<- PositionDataFrame: data frame with spatial position metadata
run<--method PositionDataFrame: data frame with spatial position metadata
run<--method SparseImagingExperiment: Pixel-sparse imaging experiments
runNames PositionDataFrame: data frame with spatial position metadata
runNames-method PositionDataFrame: data frame with spatial position metadata
runNames-method SparseImagingExperiment: Pixel-sparse imaging experiments
runNames<- PositionDataFrame: data frame with spatial position metadata
runNames<--method PositionDataFrame: data frame with spatial position metadata
runNames<--method SparseImagingExperiment: Pixel-sparse imaging experiments

-- S --

sampleNames-method IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
sampleNames-method iSet: Class to contain high-throughput imaging experiment data and metadata
sampleNames<--method IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
sampleNames<--method iSet: Class to contain high-throughput imaging experiment data and metadata
samples-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanDirection MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanDirection-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanDirection-method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scanDirection<- MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanDirection<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanDirection<--method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scanPattern MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanPattern-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanPattern-method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scanPattern<- MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanPattern<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanPattern<--method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scanPolarity MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanPolarity-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanPolarity-method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scanPolarity<- MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanPolarity<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanPolarity<--method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scans-method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scanType MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanType-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanType-method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scanType<- MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanType<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanType<--method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
select-method Deprecated functions and methods in Cardinal
select-method Data transformation and summarization for imaging experiments
selectROI Select regions-of-interest of an imaging dataset
selectROI-method Select regions-of-interest of an imaging dataset
selectROI-methods Select regions-of-interest of an imaging dataset
show-method Binmat: On-disk matrix class using on-demand disk access
show-method Hashmat: Sparse matrix class using lists as hash tables
show-method ImageData: Class containing arrays of imaging data
show-method ImagingExperiment: Abstract class for imaging experiments
show-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
show-method MSImageProcess: Class containing mass spectral preprocessing information
show-method MSImagingExperiment: Mass spectrometry imaging experiments
show-method ResultSet: Class to contain analysis results for imaging experiments
show-method SparseImagingExperiment: Pixel-sparse imaging experiments
show-method XDataFrame: DataFrame with eXtra metadata columns
SImageData SImageData: Class containing sparse image data
SImageData-class SImageData: Class containing sparse image data
SImageSet SIMageSet: Class to contain pixel-sparse imaging data
SImageSet-class SIMageSet: Class to contain pixel-sparse imaging data
SimpleImageArrayList-class ImageList: Abstract image data list
SimpleImageList-class ImageList: Abstract image data list
smoothing MSImageProcess: Class containing mass spectral preprocessing information
smoothing-method MSImageProcess: Class containing mass spectral preprocessing information
smoothing-method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
smoothing<- MSImageProcess: Class containing mass spectral preprocessing information
smoothing<--method MSImageProcess: Class containing mass spectral preprocessing information
smoothing<--method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
smoothSignal Smooth the spectra of a spectral imaging dataset
smoothSignal-method Smooth the spectra of a spectral imaging dataset
smoothSignal-methods Smooth the spectra of a spectral imaging dataset
smoothSignal.gaussian Smooth the spectra of a spectral imaging dataset
smoothSignal.ma Smooth the spectra of a spectral imaging dataset
smoothSignal.sgolay Smooth the spectra of a spectral imaging dataset
softwareName MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
softwareName-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
softwareName<- MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
softwareName<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
softwareVersion MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
softwareVersion-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
softwareVersion<- MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
softwareVersion<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
SparseImagingExperiment SparseImagingExperiment: Pixel-sparse imaging experiments
SparseImagingExperiment-class SparseImagingExperiment: Pixel-sparse imaging experiments
spatialKMeans Spatially-aware k-means clustering
SpatialKMeans-class Spatially-aware k-means clustering
spatialKMeans-method Spatially-aware k-means clustering
spatialKMeans-methods Spatially-aware k-means clustering
spatialShrunkenCentroids Spatially-aware shrunken centroid clustering and classification
SpatialShrunkenCentroids-class Spatially-aware shrunken centroid clustering and classification
spatialShrunkenCentroids-method Spatially-aware shrunken centroid clustering and classification
spatialShrunkenCentroids-methods Spatially-aware shrunken centroid clustering and classification
specimenOrigin MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
specimenOrigin-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
specimenOrigin<- MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
specimenOrigin<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
specimenType MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
specimenType-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
specimenType<- MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
specimenType<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
spectra MSImagingExperiment: Mass spectrometry imaging experiments
spectra-method MSImageSet: Class to contain mass spectrometry imaging experiment data
spectra-method MSImagingExperiment: Mass spectrometry imaging experiments
spectra-methods MSImagingExperiment: Mass spectrometry imaging experiments
spectra<- MSImagingExperiment: Mass spectrometry imaging experiments
spectra<--method MSImageSet: Class to contain mass spectrometry imaging experiment data
spectra<--method MSImagingExperiment: Mass spectrometry imaging experiments
spectrumRepresentation MSImageProcess: Class containing mass spectral preprocessing information
spectrumRepresentation-method MSImageProcess: Class containing mass spectral preprocessing information
spectrumRepresentation-method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
spectrumRepresentation<- MSImageProcess: Class containing mass spectral preprocessing information
spectrumRepresentation<--method MSImageProcess: Class containing mass spectral preprocessing information
spectrumRepresentation<--method MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
stainingMethod MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
stainingMethod-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
stainingMethod<- MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
stainingMethod<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
standardizeRuns Standardize between runs in an imaging dataset
standardizeRuns-method Standardize between runs in an imaging dataset
standardizeRuns-methods Standardize between runs in an imaging dataset
standardizeRuns.sum Standardize between runs in an imaging dataset
standardizeSamples Deprecated functions and methods in Cardinal
storageMode-method ImageData: Class containing arrays of imaging data
storageMode-method iSet: Class to contain high-throughput imaging experiment data and metadata
storageMode<--method ImageData: Class containing arrays of imaging data
storageMode<--method iSet: Class to contain high-throughput imaging experiment data and metadata
summarize-method Data transformation and summarization for imaging experiments
summary-method Orthogonal partial least squares
summary-method Principal components analysis
summary-method Partial least squares
summary-method Apply cross-validation to imaging analyses
summary-method iSet: Class to contain high-throughput imaging experiment data and metadata
summary-method Spatially-aware k-means clustering
summary-method Spatially-aware shrunken centroid clustering and classification

-- T --

tissueThickness MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
tissueThickness-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
tissueThickness<- MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
tissueThickness<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
tissueWash MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
tissueWash-method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
tissueWash<- MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
tissueWash<--method MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
tolerance-method MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
tolerance<--method MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
topLabels Retrieve top-ranked features from analysis results
topLabels-method Retrieve top-ranked features from analysis results
topLabels-methods Retrieve top-ranked features from analysis results

-- V --

varLabels-method iSet: Class to contain high-throughput imaging experiment data and metadata
varLabels<--method iSet: Class to contain high-throughput imaging experiment data and metadata
varMetadata-method iSet: Class to contain high-throughput imaging experiment data and metadata
varMetadata<--method iSet: Class to contain high-throughput imaging experiment data and metadata

-- W --

writeAnalyze Write mass spectrometry imaging data files
writeAnalyze-method Write mass spectrometry imaging data files
writeImzML Write mass spectrometry imaging data files
writeImzML-method Write mass spectrometry imaging data files
writeMSIData Write mass spectrometry imaging data files
writeMSIData-method Write mass spectrometry imaging data files

-- X --

XDataFrame XDataFrame: DataFrame with eXtra metadata columns
XDataFrame-class XDataFrame: DataFrame with eXtra metadata columns

-- misc --

$-method ImagingExperiment: Abstract class for imaging experiments
$-method ResultSet: Class to contain analysis results for imaging experiments
$-method iSet: Class to contain high-throughput imaging experiment data and metadata
$<--method ImagingExperiment: Abstract class for imaging experiments
$<--method XDataFrame: DataFrame with eXtra metadata columns
$<--method iSet: Class to contain high-throughput imaging experiment data and metadata
%>% Objects exported from other packages
[-method Binmat: On-disk matrix class using on-demand disk access
[-method Hashmat: Sparse matrix class using lists as hash tables
[-method IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
[-method ImageList: Abstract image data list
[-method MSContinuousImagingExperiment: Dense mass spectrometry imaging experiments
[-method MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
[-method MassDataFrame: data frame with mass-to-charge ratio metadata
[-method PositionDataFrame: data frame with spatial position metadata
[-method ResultSet: Class to contain analysis results for imaging experiments
[-method SImageData: Class containing sparse image data
[-method SIMageSet: Class to contain pixel-sparse imaging data
[-method SparseImagingExperiment: Pixel-sparse imaging experiments
[<--method Hashmat: Sparse matrix class using lists as hash tables
[<--method ImageList: Abstract image data list
[<--method SparseImagingExperiment: Pixel-sparse imaging experiments
[[-method ImageData: Class containing arrays of imaging data
[[-method ImageList: Abstract image data list
[[-method ImagingExperiment: Abstract class for imaging experiments
[[-method ResultSet: Class to contain analysis results for imaging experiments
[[-method iSet: Class to contain high-throughput imaging experiment data and metadata
[[<--method ImageData: Class containing arrays of imaging data
[[<--method ImageList: Abstract image data list
[[<--method ImagingExperiment: Abstract class for imaging experiments
[[<--method MSContinuousImagingExperiment: Dense mass spectrometry imaging experiments
[[<--method MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
[[<--method XDataFrame: DataFrame with eXtra metadata columns
[[<--method iSet: Class to contain high-throughput imaging experiment data and metadata